use super::*;
use molframe_core::io::InputBuffer;
use molframe_core::structure::AtomRef;
use std::fmt::Write as _;
#[test]
fn common_records_do_not_retain_atom_lines() {
let text = "HEADER EXAMPLE\nATOM 1 N GLY A 1 1.000 1.000 1.000 1.00 0.00 N\nCONECT 1 2\n";
let mut common = CommonRecords::new();
for line in Lines::new(text) {
common.observe(&line.expect("line"));
}
assert_eq!(common.lines.len(), 2);
assert_eq!(fixed::record(common.lines[0].text), "HEADER");
assert_eq!(fixed::record(common.lines[1].text), "CONECT");
}
#[test]
fn many_ragged_models_are_materialised_in_deposition_order() {
let mut text = String::new();
for model in 1..=128 {
let atom = if model == 128 { " O " } else { " N " };
let written = writeln!(
text,
"MODEL {model:4}\nATOM 1 {atom} GLY A 1 1.000 1.000 1.000 1.00 0.00 N\nENDMDL"
);
assert!(written.is_ok());
}
let input = InputBuffer::from_bytes(text.into_bytes());
let (structure, _) = crate::read(&input, &ReadOptions::new())
.unwrap_or_else(|findings| panic!("read failed: {findings:?}"));
let Some(models) = structure.ragged_models() else {
panic!("the final identity change must select ragged storage");
};
assert_eq!(models.len(), 128);
let numbers: Vec<_> = structure
.data()
.models()
.filter_map(molframe_core::structure::ModelRef::number)
.collect();
assert_eq!(numbers.first(), Some(&1));
assert_eq!(numbers.last(), Some(&128));
}
#[test]
fn per_model_occupancy_and_b_factor_stay_dense_and_are_reported_once() {
let text = "MODEL 1\nATOM 1 N GLY A 1 1.000 1.000 1.000 1.00 10.00 N\nENDMDL\nMODEL 2\nATOM 1 N GLY A 1 2.000 2.000 2.000 0.50 20.00 N\nENDMDL\nMODEL 3\nATOM 1 N GLY A 1 3.000 3.000 3.000 0.25 30.00 N\nENDMDL\n";
let input = InputBuffer::from_bytes(text.as_bytes().to_vec());
let (structure, findings) = crate::read(&input, &ReadOptions::new())
.unwrap_or_else(|findings| panic!("read failed: {findings:?}"));
assert!(structure.ragged_models().is_none());
assert_eq!(structure.model_count(), 3);
let atom = structure.data().atoms().next().expect("one atom");
assert_eq!(atom.occupancy(), Some(1.0));
assert_eq!(atom.b_factor(), Some(10.0));
let noted = findings
.iter()
.filter(|finding| finding.code() == molframe_core::diagnostic::Code::W3015)
.count();
assert_eq!(noted, 1);
}
#[test]
fn a_non_coordinate_identity_change_selects_independent_annotations() {
let text = "MODEL 1\nATOM 1 N GLY A 1 1.000 1.000 1.000 1.00 10.00 N\nENDMDL\nMODEL 2\nATOM 1 O GLY A 1 2.000 2.000 2.000 0.50 20.00 O\nENDMDL\n";
let input = InputBuffer::from_bytes(text.as_bytes().to_vec());
let (structure, _) = crate::read(&input, &ReadOptions::new())
.unwrap_or_else(|findings| panic!("read failed: {findings:?}"));
let Some(models) = structure.ragged_models() else {
panic!("an atom identity change must be ragged");
};
let occupancies: Vec<_> = models
.iter()
.filter_map(|model| model.data().atoms().next().and_then(AtomRef::occupancy))
.collect();
assert_eq!(occupancies, [1.0, 0.5]);
}
#[test]
fn ragged_models_receive_shared_metadata_and_connectivity() {
use crate::PdbHeadersExt as _;
let text = "HEADER TEST 01-JAN-00 9XYZ\nCRYST1 10.000 11.000 12.000 90.00 90.00 90.00 P 1\nMODEL 1\nATOM 1 N GLY A 1 1.000 1.000 1.000 1.00 10.00 N\nATOM 2 C GLY A 1 2.000 2.000 2.000 1.00 10.00 C\nENDMDL\nMODEL 2\nATOM 1 O GLY A 1 1.000 1.000 1.000 1.00 10.00 O\nATOM 2 C GLY A 1 2.000 2.000 2.000 1.00 10.00 C\nENDMDL\nCONECT 1 2\n";
let input = InputBuffer::from_bytes(text.as_bytes().to_vec());
let (structure, _) = crate::read(&input, &ReadOptions::new())
.unwrap_or_else(|findings| panic!("read failed: {findings:?}"));
let Some(models) = structure.ragged_models() else {
panic!("identity-changing models must be ragged");
};
assert!(models.iter().all(|model| model.data().bonds.len() == 1));
assert!(models.iter().all(|model| model.data().cell.is_some()));
assert!(structure.pdb_headers().is_some());
}
#[test]
fn a_ragged_pdb_ensemble_is_refused_by_the_model_guard() {
let text = "MODEL 1\nATOM 1 N GLY A 1 1.000 1.000 1.000 1.00 10.00 N\nENDMDL\nMODEL 2\nATOM 1 O GLY A 1 2.000 2.000 2.000 1.00 20.00 O\nENDMDL\n";
let input = InputBuffer::from_bytes(text.as_bytes().to_vec());
let (structure, _) = crate::read(&input, &ReadOptions::new())
.unwrap_or_else(|findings| panic!("read failed: {findings:?}"));
assert!(structure.is_ragged_ensemble());
// The outer shell has no atoms of its own, so an unguarded analysis sees an
// empty molecule; the guard turns that into an explicit refusal.
assert_eq!(structure.data().atoms().count(), 0);
let Err(finding) = structure.require_resolved_model() else {
panic!("a ragged ensemble must be refused");
};
assert_eq!(finding.code(), molframe_core::diagnostic::Code::E6003);
let Some((model, _)) = structure.model_snapshot(molframe_core::index::ModelIndex::new(1))
else {
panic!("model 2 exists");
};
assert!(model.require_resolved_model().is_ok());
assert_eq!(model.data().atoms().count(), 1);
}